Computational Systems Biology
Sauro Lab
University of Washington
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6. Optimization
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maintained by Frank Bergmann
 
 
 
 

SBML Layout Support Module API

Service: reader

byte[] getImage()

Returns the currently loaded image as byte-stream.

byte[] getScaledImage(double)

Returns the currently loaded image scaled with the given scale factor as byte-stream.

string getVersion()

SBML Layout Viewer/Manipulator version 0.2

void setVisible(boolean)

Hides/Shows the Form

void doAnalysis(string)

Renders the layout of the given SBML model

void loadSBML(string)

Loads a new SBML model

string getSBML()

Returns the original model

boolean hasLayout()

Test's whether the loaded SBML has Layout Information

int getNumberOfLayouts()

Returns the number of supported Layouts in this model

void setCurrentLayout(int)

Selects a different layout as the current Layout

string[] getInfo()

Returns information about the currently loaded Layout

int getNumberOfCompartmentGlyphs()

Returns the number of compartment glyphs in default layout

int getNumberOfReactionGlyphs()

Returns the number of reaction glyphs in default layout

int getNumberOfSpeciesGlyphs()

Returns the number of species glyphs in default layout

int getNumberOfAliasNodes(string)

Returns the number of alias nodes for the given species glyph id in default layout

int getNumberOfTextGlyphs()

Returns the number of text glyphs in default layout

string getLayoutId()

Returns the identifier of the currently selected layout

double[] getDimensions()

Returns the dimension of the default layout (Format: width, height, depth)

void setLayout(string,double[])

Sets the Id and dimension of the current layout

{} getCompartmentGlyph(int)

Returns Layout information for the compartment glyph at the given index position. (Format: id, reference, double[] position, double[] dimension)

{} getCompartmentGlyphById(string)

Returns Layout information for the Compartment Glyph with the given id (sbml level2) or name (sbml level1). (Format: id, reference, double[] position, double[] dimension)

boolean hasCompartmentGlyphForID(string)

Tests whether a given compartmentGlyph exists for a given id

int getCompartmentGlyphIndexById(string)

Returns the index for the Compartment Glyph with the given id (sbml level2) or name (sbml level1).

void setCompartmentGlyph(int,string,string,double[],double[])

Sets id, reference and bounding box of the i-th compartment glyph. (Format: index, id, reference, double[] position, double[] dimension)

void addCompartmentGlyph(string,string,double[],double[])

Adds a new Compartment Glyph. (Format: index, id, reference, double[] position, double[] dimension)

void removeCompartmentGlyph(int)

Removes the i-th Compartment Glyph.

{} getReactionGlyphRenderInfo(int)

Returns Thickness and Color information of the given Reaction Glyph ID in JD2 format

double[] getReactionGlyphRenderInfoGL(int)

Returns Thickness and Color information of the given Reaction Glyph ID in form of a double array [ thickness, red, green, blue, alpha)

string getSpeciesGlyphRenderInfo(int)

Returns the Rendering information of a Species Glyph in JD2 XML

string getTextGlyphRenderInfo(int)

Returns the Rendering information of a Text Glyph in JD2 XML

{} getSpeciesGlyph(int)

Returns Layout information for the Species Glyph at the given index position. (Format: id, reference, double[] position, double[] dimension)

double[] getSpeciesGlyphColor(int)

Returns Returns the currently used Color for the SpeciesGlyph with the given index (Format: alpha,red,green,blue as double between 0 and 1)

{} getSpeciesGlyphById(string)

Returns Layout information for the Species Glyph with the given id (sbml level2) or name (sbml level1). (Format: id, reference, double[] position, double[] dimension)

int getSpeciesGlyphIndexById(string)

Returns the index for the Species Glyph with the given id (sbml level2) or name (sbml level1).

void setSpeciesGlyph(int,string,string,double[],double[])

Sets the i-th Species Glyph (Format: index, id, reference, double[] position, double[] dimension)

void addSpeciesGlyph(string,string,double[],double[])

Adds a new Species Glyph (Format: id, reference, double[] position, double[] dimension)

void removeSpeciesGlyph(int)

Removes the i-th Species Glyph

{} getAliasNode(string,int)

Returns the Alias node for the given SpeciesGlyphId and index (Format: aliasId, double[] position, double[] dimension)

void setAliasNode(string,double[],double[])

sets the aliasnode with the given id (Format: aliasId, double[] position, double[] dimension)

void addAliasNode(string,string,double[],double[])

adds a new alias node (Format: aliasId, reference, double[] position, double[] dimension)

{} getTextGlyph(int)

Returns Layout information for the TextGlyph at the given position. (Format: id, reference, text, double[] position, double[] dimension)

void setTextGlyph(int,string,string,string,double[],double[])

Sets the i-th TextGlyph (Format: index, id, reference, text, double[] position, double[] dimension)

void addTextGlyph(string,string,string,double[],double[])

Adds a new TextGlyph (Format: index, id, reference, text, double[] position, double[] dimension)

void removeTextGlyph(int)

Removes the i-th Text Glyph

{} getReactionGlyph(int)

Returns Layout information on the ReactionGlyph at the given position. (Format: id, reference, numberOfSpeciesReferences, double[] position, double[] dimension)

{} getReactionGlyphById(string)

Returns Layout information on the ReactionGlyph with the given id (sbml level2) or name (sbml level1). (Format: id, reference, numberOfSpeciesReferences, double[] position, double[] dimension)

void setReactionGlyph(int,string,string,double[],double[])

Set's the i-th ReactionGlyph (Format: index, id, reference, double[] position, double[] dimension)

int addReactionGlyph(string,string,double[],double[])

Adds a new ReactionGlyph and returns the id. (Format: id, reference, double[] position, double[] dimension)

void removeReactionGlyph(int)

Removes the i-th Reaction Glyph.

{}[] getReactionCurve(int)

Returns the curve description for the ith reaction glyph. (Format: array of (type, double[] start, double[] end, double[] base1, double[] base2))

void setReactionCurve(int,{}[])

Sets the curve description for the i-th reaction glyph. (Format: index, array of (type, double[] start, double[] end, double[] base1, double[] base2))

{} getSpeciesReference(int,int)

Returns the SpeciesReference for the i-th reaction and j-th species reference. (Format: id, reference, speciesglyph, role)

void setSpeciesReference(int,int,string,string,string,string)

sets the SpeciesReference for the i-th reaction and j-th species reference. (Format: reaction index, reference index, id, reference, speciesglyph, role)

int addSpeciesReference(int,string,string,string,string)

Adds a new Species reference and returns the handle. (Format: reaction index, id, reference, speciesglyph, role)

void removeSpeciesReference(int,int)

Removes the SpeciesReference for the i-th reaction and j-th species reference.

{}[] getSpeciesReferenceCurve(int,int)

Returns the SpeciesReference Curve for the i-th reaction and j-th species reference. (Format: array of (type, double[] start, double[]end, double[] base1, double[] base2))

void setSpeciesReferenceCurve(int,int,{}[])

Sets the SpeciesReference Curve for the i-th reaction and j-th species reference. (Format: reaction index, reference index, array of (type, double[] start, double[] end, double[] base1, double[] base2))

string writeSBML()

Returns a new SBML document with the SBML Layout Extension

 
sbw/sbmllayout/api.txt · Last modified: 2007/01/12 08:22 (external edit)
 

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